Help:Frequently Asked Questions
From WikiPathways
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==== I am working on a pathway for a publication, and I don't want to share it with the rest of the community just yet. Can I still author my pathway at WikiPathways? ==== | ==== I am working on a pathway for a publication, and I don't want to share it with the rest of the community just yet. Can I still author my pathway at WikiPathways? ==== | ||
Yes! WikiPathways supports the notion of private pathways that are visible only to the author and hidden for the rest of the community. You can designate a pathway as private when you first create it. For details on this topic, see the section on [[:Help:Private Pathways|Private Pathways]]. | Yes! WikiPathways supports the notion of private pathways that are visible only to the author and hidden for the rest of the community. You can designate a pathway as private when you first create it. For details on this topic, see the section on [[:Help:Private Pathways|Private Pathways]]. | ||
| - | ==== I want to use one of the pathways in GenMAPP, but since I am not on a PC, | + | ==== I want to use one of the pathways in GenMAPP, but since I am not on a PC, download the MAPP or exporting to MAPP doesn't work. How can I get a pathway in GenMAPP format? ==== |
| - | On the ''Pathway Page'', click the '' | + | On the ''Pathway Page'', click the ''Download'' button and select the gpml format. Go to [http://www.pathvisio.org PathVisio] and download the PathVisio program. In PathVisio, open the gpml version of the pathway, then select ''File > Export'' to export the pathway in .mapp format. |
==== It's difficult to view large pathways in the editor window. Is there a way to increase the size of the editor window? ==== | ==== It's difficult to view large pathways in the editor window. Is there a way to increase the size of the editor window? ==== | ||
In the editor, click the '' Switch to full-screen mode'' button in the tool bar. This will open a separate editor window that can be resized to fit the whole pathway. | In the editor, click the '' Switch to full-screen mode'' button in the tool bar. This will open a separate editor window that can be resized to fit the whole pathway. | ||
Revision as of 18:48, 9 April 2009
General
Who, What and Why is WikiPathways?
See About WikiPathways.
Where does the pathway content at WikiPathways come from?
At the start of WikiPathways, the pathway content mirrored that of GenMAPP.org, which was originally contributed by the GenMAPP user community. The content has since grown by contributions from the community.
How do I cite pathways from WikiPathways?
See our License and Terms of Use
How many pathways are part of WikiPathways?
Pathway statistics per species are published on our Home page.
Does WikiPathways check the content of contributed pathways for quality and accuracy?
No, WikiPathways does not review pathway content, except to look for vandalism and obvious problems.
How is WikiPathways different from KEGG, Reactome, BioCarta, Pathway Commons and other online pathway resources?
In addition to viewing and distributing pathways, WikiPathways content is also fully editable directly on the website. This is possible since WikiPathways is based on a wiki platform, similar to Wikipedia. For a complete list of pathway resources, see Pathguide.
What is GPML?
GPML is the file format used to store pathway content at WikiPathways. GPML is short for GenMAPP Pathway Markup Language and it is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio.
Using WikiPathways
How can I use the pathway content from WikiPathways?
In addition to browsing and editing the content online, WikiPathways content can be downloaded in multiple formats for a variety of purposes:
- Pathways in GPML format can be used in the PathVisio program for editing.
- Pathways at WikiPathways can be opened in the Cytoscape program for network analysis purposes.
- Pathways in SVG, PNG and PDF graphical formats can be directly incorporated into presentations and publications.
- Pathways in MAPP format can be exported from the WikiPathways editor and used in GenMAPP program for integrating pathway information with data and for data over-representation analysis on collections of pathways. Note: MAPP export currently works only under the Windows operating system.
- Pathways can be downloaded in PWF format for use with the Eu.Gene tool.
How can I download all pathways at WikiPathways?
Batch download of pathways in gpml pdf, pwf, svg, png and txt formats is available here: Batch Download. A flat file of all pathways is also available on the batch download page in both html and txt format.
I created a pathway and made a mistake in it, how can I correct it?
You can revert the changes to your pathways under the History section of the Pathway page.
I want to delete a pathway, but there is no option for deleting.
You can delete a pathway only if you are the sole author of the pathway. For details on deleting a pathway, see Deleting Pathways.
I am working on a pathway for a publication, and I don't want to share it with the rest of the community just yet. Can I still author my pathway at WikiPathways?
Yes! WikiPathways supports the notion of private pathways that are visible only to the author and hidden for the rest of the community. You can designate a pathway as private when you first create it. For details on this topic, see the section on Private Pathways.
I want to use one of the pathways in GenMAPP, but since I am not on a PC, download the MAPP or exporting to MAPP doesn't work. How can I get a pathway in GenMAPP format?
On the Pathway Page, click the Download button and select the gpml format. Go to PathVisio and download the PathVisio program. In PathVisio, open the gpml version of the pathway, then select File > Export to export the pathway in .mapp format.
It's difficult to view large pathways in the editor window. Is there a way to increase the size of the editor window?
In the editor, click the Switch to full-screen mode button in the tool bar. This will open a separate editor window that can be resized to fit the whole pathway.
Where can I report bugs?
Please report any bugs you encounter and submit any general comments to our Google group. You can also report bugs directly to our bug tracker. Also check our known problems to see if your problem is a known issue.
